Using coupled hidden markov chains to estimate colonization and seed bank survival in a metapopulation of annual plants

The study of ecological systems is often impeded by components that escape perfect observation, such as the trajectories of moving animals or the status of plant seed banks. These hidden components can be efficiently handled with statistical modeling by using hidden variables, which are often called latent variables.Notably, the hidden variables framework enables us to model an underlying interaction structure between variables (including random effects in regression models) and perform data clustering, which are useful tools in the analysis of ecological data.This book provides an introduction to hidden variables in ecology, through recent works on statistical modeling as well as on estima…